On the construction of LIECE models for the serotonin receptor 5-HT[Formula: see text] R

Computer-aided approaches to ligand design need to balance accuracy with speed. This is particularly true for one of the key parameters to be optimized during ligand development, the free energy of binding ([Formula: see text] G[Formula: see text] ). Here, we developed simple models based on the Lin...

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Detalles Bibliográficos
Autores principales: Shahraki, Aida, Selent, Jana, Kolb, Peter
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer International Publishing 2023
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10276788/
https://www.ncbi.nlm.nih.gov/pubmed/37312012
http://dx.doi.org/10.1007/s10822-023-00507-3
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author Shahraki, Aida
Selent, Jana
Kolb, Peter
author_facet Shahraki, Aida
Selent, Jana
Kolb, Peter
author_sort Shahraki, Aida
collection PubMed
description Computer-aided approaches to ligand design need to balance accuracy with speed. This is particularly true for one of the key parameters to be optimized during ligand development, the free energy of binding ([Formula: see text] G[Formula: see text] ). Here, we developed simple models based on the Linear Interaction Energy approximation to free energy calculation for a G protein-coupled receptor, the serotonin receptor 2A, and critically evaluated their accuracy. Several lessons can be taken from our calculations, providing information on the influence of the docking software used, the conformational state of the receptor, the cocrystallized ligand, and its comparability to the training/test ligands. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10822-023-00507-3.
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spelling pubmed-102767882023-06-19 On the construction of LIECE models for the serotonin receptor 5-HT[Formula: see text] R Shahraki, Aida Selent, Jana Kolb, Peter J Comput Aided Mol Des Article Computer-aided approaches to ligand design need to balance accuracy with speed. This is particularly true for one of the key parameters to be optimized during ligand development, the free energy of binding ([Formula: see text] G[Formula: see text] ). Here, we developed simple models based on the Linear Interaction Energy approximation to free energy calculation for a G protein-coupled receptor, the serotonin receptor 2A, and critically evaluated their accuracy. Several lessons can be taken from our calculations, providing information on the influence of the docking software used, the conformational state of the receptor, the cocrystallized ligand, and its comparability to the training/test ligands. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10822-023-00507-3. Springer International Publishing 2023-06-14 2023 /pmc/articles/PMC10276788/ /pubmed/37312012 http://dx.doi.org/10.1007/s10822-023-00507-3 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Shahraki, Aida
Selent, Jana
Kolb, Peter
On the construction of LIECE models for the serotonin receptor 5-HT[Formula: see text] R
title On the construction of LIECE models for the serotonin receptor 5-HT[Formula: see text] R
title_full On the construction of LIECE models for the serotonin receptor 5-HT[Formula: see text] R
title_fullStr On the construction of LIECE models for the serotonin receptor 5-HT[Formula: see text] R
title_full_unstemmed On the construction of LIECE models for the serotonin receptor 5-HT[Formula: see text] R
title_short On the construction of LIECE models for the serotonin receptor 5-HT[Formula: see text] R
title_sort on the construction of liece models for the serotonin receptor 5-ht[formula: see text] r
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10276788/
https://www.ncbi.nlm.nih.gov/pubmed/37312012
http://dx.doi.org/10.1007/s10822-023-00507-3
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